The Justice Department is investigating Harvard University’s use of race in admissions, and is warning the school that it is out of compliance with federal civil rights law because it has not provided documents the department requested.

In two letters sent Friday, Justice Department officials said that Harvard had not produced “a single document” that had been requested, despite a Nov. 2 deadline, and that the university’s attorney had tried to “side-step Harvard’s Title VI obligations.” Because Harvard receives that federal funding under the Civil Rights Act of 1964, department officials argue, the university must comply with its request. Title VI, part of the Civil Rights Act, prohibits discrimination on the basis of race, color and national origin in programs that receive federal funding.

The confirmation of the investigation, first reported by the Wall Street Journal, followed months of signaling from the department that it would challenge affirmative action policies.

The highly charged question — battled in multiple U.S. Supreme Court cases — is whether colleges can consider an applicant’s race as a factor in admissions.

The Supreme Court has ruled repeatedly on affirmative action cases in higher education, most recently in June 2016, when it upheld a University of Texas policy that enables race to be a factor in admission decisions. That 4-to-3 ruling was widely interpreted as a green light for the use of race conscious policies in what schools such as Harvard call “holistic” admissions. But critics said the ruling was narrow enough that other lawsuits could be filedto challenge affirmative action.

“As we have repeatedly made clear to the Department of Justice, the university will certainly comply with its obligations under Title VI,” Anna Cowenhoven, a spokeswoman for Harvard, said in a written statement.

“In the process, we have an obligation to protect the confidentiality of student and applicant files and other highly sensitive records, and we have been seeking to engage the Department of Justice in the best means of doing so.”

“The Department of Justice takes seriously any potential violation of an individual’s civil and constitutional rights, but we will not comment at this time,” department spokesman Devin M. O’Malley said in an email.

A pending lawsuit brought by an advocacy group, Students for Fair Admissions, asked a federal judge to prohibit the use of race in future undergraduate admissions decisions by Harvard, claiming the school violates federal civil rights law and intentionally discriminates against Asian American students.

Edward Blum, president of Students for Fair Admissions, sent a written statement Tuesday saying his group is gratified that the department had launched an investigation. “For decades, Harvard has unfairly and unlawfully restricted the number of Asians it admits.

“Harvard’s Asian quotas, and the overall racial balancing that follows, have been ignored by our federal agencies for too long. This investigation is a welcome development.”

In a letter sent Friday, Matthew Donnelly of the Justice Department’s Civil Rights Division said Waxman had erroneously challenged the agency’s right to investigate Harvard under Title VI and had proposed a plan to give restricted access to limited documents. He also wrote that the university has the documents readily available because it already produced them for the plaintiffs in the civil suit.

In a separate letter, John M. Gore, acting assistant attorney general in theCivil Rights Division, said that more than two months had passed without Harvard supplying a single document, and that the university was out of compliance with its obligations under Title VI.

Waxman had written to Gore in early October saying university officials are well aware of their obligations under Title VI. But he said the opening of an investigation under such circumstances was so outside of normal practices that the university wished to clarify the authority and rationale for the department’s decision. He pointed out that identical issues are being litigated in federal court, and that Title VI requires a “prompt” investigation, but the complaint that triggered the investigation apparently had been brought 2½ years earlier.

Waxman asked for copies of written correspondence about Harvard between relevant department officials and groups including Students for Fair Admissions and their attorneys. And he asked for a proposal of how to safeguard the privacy of sensitive information, such as students’ applications and the university’s candid evaluations.

In an email to Gore on Nov. 7, Waxman sent a proposal to comply with the request, saying the university was willing to explore with the department a confidentiality agreement. He also continued to question aspects of an investigation he characterized as “irregular.”

Anurima Bhargava, who was chief of the educational opportunity section in the Justice Department’s civil rights division under the Obama administration, said Tuesday the department’s actions appeared unusual because federal education officials had already considered the issue in 2015 and decided not to pursue it.

“It’s peculiar that you have a situation in which the Department of Education has dismissed a complaint and the Justice Department then decides to investigate under Title VI,” Bhargava said. She said it was also unusual for the Justice Department to conduct a “parallel investigation” when a federal suit is pending on a similar set of allegations. Bhargava recently held fellowships at the Harvard Kennedy School, but she said she is not currently affiliated with the school.

The Harvard admissions process routinely draws public attention because the Ivy League university is one of the most selective in the world. In March, 2,056 students were offered admission to the fall 2017 freshman class, out of 39,506 applicants. That translates to an admission rate of little more than 5 percent.

Of those admitted, 22.2 percent were Asian American, the university said, while 14.6 percent were African American, 11.6 percent Latino and 1.9 percent Native American.